Molecular dynamics and free energy simulation methodologies have been employed to investigate the structure, flexibility and dynamics of a variety of protein and nucleic acid systems in solution. Solvated molecular dynamics simulations give realistic information into sequence specific nucleic acid structure, hydration and dynamics which give insight into function. Continuum methods have been applied as an analysis tool to give insight into the relative energetics of a variety of systems. The focus of our work is the development of accurate force field parameters and dependence of the environment on nucleic acid structure. We are using MidasPlus extensively as our visualization tool.